Plant breeding depends on efficient exploitation of genetic variation, residing in the germplasm of a particular crop species, which determines the phenotype of a plant within a specific environment. Whereas this is traditionally done by selection of a combination of desirable traits observed at the phenotypic level, this can increasingly be performed by selection on the basis of molecular markers which are genetically closely linked to the allelic form of a gene which contributes to the expression of a specific trait.
Selection of traits on the basis of molecular markers is independent of the developmental stage of a plant and independent of the environment, which significantly enhances the selection process. The number of traits including complex traits controlled by multiple genes which can be selected upon using molecular markers has strongly increased and it can be envisaged that this development will continue at increasing pace.
Another tendency in the field of plant breeding arises form reverse genetics. Reverse genetics relates to an approach in which genes are isolated and their function is determined by modifying their primary structure or expression. With the current increase in knowledge on gene function, especially in model systems like Arabidopsis thaliana, reverse genetics approaches in crop systems currently gain in efficacy.
In order to determine allelic variability of candidate genes a plethora of DNA diagnostic tools are available and known to the person skilled in the art. Large populations of plants containing natural or induced allelic variation need to be screened for DNA polymorphisms at the locus of interest to acquire a saturated collection of allelic variants. Allelic forms of genes thus found can be assessed for their contribution to a plant phenotype by association studies.
The cost of screening breeding or mutant populations is largely determined by labour required to grow and sample individual plants of the population under investigation and to prepare DNA from these samples. In case a population is made available as seed samples representing the genetic variation residing within individual plants of the population under investigation, significant labour has been invested in harvesting seeds plant by plant as related individuals in families. Moreover, this exercise requires reiteration for each additional population being produced and assessed for allelic variants at specific genetic loci.